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Sample GSM1018508 Query DataSets for GSM1018508
Status Public on Mar 27, 2013
Title Spleen Mock infected 6h Rep 2 (89-1591)
Sample type RNA
 
Source name Spleen Mock infected 6h
Organism Mus musculus
Characteristics strain: C57BL/6
tissue: Spleen
gender: Female
Treatment protocol Mice were infected for 6h with 5 x 10^7 CFU of Streptococcus suis strain 89-1591 or mock-infected with bacterial growth medium (THB).
Growth protocol Bacterial culture was prepared by transferring 10 μl of 1/1,000 dilutions of 8-h cultures into 30 ml of THB, which was incubated for 16 h at 37°C without agitation. Stationary-phase bacteria were washed twice in PBS (pH 7.3). The bacterial pellet was then resuspended and adjusted to a concentration of 5 × 10^8 c.f.u. ml-1.
Extracted molecule total RNA
Extraction protocol RNA was homogenized from RNAlater-stabilized spleen tissus, extracted and DNAse I treated using QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.
Label Biotin
Label protocol Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays
 
Hybridization protocol Standard Illumina hybridization protocol
Scan protocol Standard Illumina scanning protocol
Description Replicate 2
Data processing The data were first raw-filtered in order to identify and remove probesets that were not detected and then normalised using robust spline normalization with FlexArray v1.6
 
Submission date Oct 11, 2012
Last update date Mar 27, 2013
Contact name Claude Lachance
E-mail(s) claude.lachance@mail.mcgill.ca
Organization name Bio-Rad
Street address 1329 Meyerside Drive
City Mississauga
State/province Ontario
ZIP/Postal code L5T 1C9
Country Canada
 
Platform ID GPL6885
Series (1)
GSE41520 Genome wide analysis of C57BL-6 mice infected with North-American strain (89-1591) of Streptococcus suis
Relations
Reanalyzed by GSM1018516
Reanalyzed by GSM1018524

Data table header descriptions
ID_REF
VALUE log2 robust spline normalized

Data table
ID_REF VALUE
ILMN_1212607 8.274331595
ILMN_1212612 8.073622532
ILMN_1212636 10.99821546
ILMN_1212637 9.354817932
ILMN_1212645 8.356776334
ILMN_1212648 9.333902791
ILMN_1212653 8.588495202
ILMN_1212672 9.081343469
ILMN_1212682 8.023213915
ILMN_1212692 8.05663996
ILMN_1212693 8.639826477
ILMN_1212695 8.051603241
ILMN_1212702 14.4979707
ILMN_1212703 8.326919972
ILMN_1212717 8.062441251
ILMN_1212720 8.311609317
ILMN_1212759 8.855240068
ILMN_1212791 8.03981479
ILMN_1212794 9.061551403
ILMN_1212828 7.859836939

Total number of rows: 13492

Table truncated, full table size 327 Kbytes.




Supplementary data files not provided
Raw data are available on Series record
Processed data included within Sample table

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